Course syllabus

Jump to today

Zoom link to today's exam.

Welcome to the MVE510 - Introduction to bioinformatics. This is the course home page and contains all the information you need to participate and complete the course.

The course will this year be held online and no physical lectures or computer exercises will be held at the Chalmers campus. More information about the course will soon be available.

 

Teachers

Erik Kristiansson, examiner, course administrator, lecturer

Juan Salvador Inda Diaz, computer exercise assistant

David Lund, computer exercise assistant

 

Student representatives

Leo Benson
Edwin Eliasson
Louise Stauber Näslund
Hannah Steinhausen
Chattarin Wangwittaya

Course aims, plan and schedule

Syllabus with course aims

Course plan (updated 2020-12-01)

Lectures

Lecture Date Time Zoom link Password
Lecture 1 November 3 13.15-15.00 https://chalmers.zoom.us/j/67396337838 454454
Lecture 2 November 6 13.15-15.00 https://chalmers.zoom.us/j/63272359873 454454
Lecture 3 November 10 13.15-15.00 https://chalmers.zoom.us/j/61010885301 454454
Lecture 4 November 13 13.15-15.00 https://chalmers.zoom.us/j/62429696152 454454
Lecture 5 November 17 13.15-15.00 https://chalmers.zoom.us/j/68379078621 454454
Lecture 6 November 20 13.15-15.00 https://chalmers.zoom.us/j/63509309213 454454
Lecture 7 November 24 13.15-15.00 https://chalmers.zoom.us/j/67368215280 454454
Lecture 8 November 27 13.15-15.00 https://chalmers.zoom.us/j/64217741260 454454
Lecture 9 December 1 13.15-15.00 https://chalmers.zoom.us/j/69727096299 454454
Lecture 10 December 4 13.15-15.00 https://chalmers.zoom.us/j/65572341810 454454

Lecture 11

Extra lecture

 December 8 13.15-15.00 https://chalmers.zoom.us/j/62488865906 454454
Lecture 12 December 11 13.15-15.00 https://chalmers.zoom.us/j/63058647380 454454
Lecture 13 Moved to December 9  10.00-11.45 https://chalmers.zoom.us/j/66378804748 454454
Lecture 14 December 18 13.15-15.00 https://chalmers.zoom.us/j/62034464362 454454

All handwritten lecture notes can be found here.

 

Computer exercises

Help list can be found here

Exercise Date Time Zoom link Password
Computer exercise Tuesday, November 3 15.15-17.00 https://chalmers.zoom.us/j/63506798878 010101
Computer exercise Wednesday, November 4 13.15-17.00 https://chalmers.zoom.us/j/63562517993 010101
Computer exercise Tuesday, November 10 15.15-17.00 https://chalmers.zoom.us/j/63594048194 010101
Computer exercise Wednesday, November 11 13.15-17.00 https://chalmers.zoom.us/j/69558888053 010101
Computer exercise Tuesday, November 17 15.15-17.00 https://chalmers.zoom.us/j/61636804225 010101
Computer exercise Wednesday, November 18 13.15-17.00 https://chalmers.zoom.us/j/61271820044 010101
Computer exercise Tuesday, November 24 15.15-17.00 https://chalmers.zoom.us/j/69102425531 010101
Computer exercise Wednesday, November 25 13.15-17.00 https://chalmers.zoom.us/j/64210669948 010101
Computer exercise Tuesday, December 1 15.15-17.00 https://chalmers.zoom.us/j/62775822139 010101
Computer exercise Wednesday, December 2 13.15-17.00 https://chalmers.zoom.us/j/69156274202 010101
Computer exercise Tuesday, December 8 15.15-17.00 https://chalmers.zoom.us/j/66248034699 010101
Computer exercise Wednesday, December 9 13.15-17.00 https://chalmers.zoom.us/j/65152810536 010101
Computer exercise Tuesday, December 15 15.15-17.00 https://chalmers.zoom.us/j/62179890042 010101
Computer exercise Wednesday, December 16 13.15-17.00 https://chalmers.zoom.us/j/68030958579 010101

 

 

Course material

Please refer to the course plan for lecture-by-lecture reading instructions.

Lecture notes

Papers

The following scientific papers are a part of the literature of this course. 

Extra exercises

Optional course book

Xinkun Wang, Next-Generation Sequencing Data Analysis, CRC Press, ISBN 9781482217889. The course covers chapters 2-5, 7-9, and 13. 

 

Computer exercises

The course contains four compulsory computer exercises. Computer exercise 1 is examined at the scheduled exercise. Computer exercise 2, 3 and 4 should be handed in as written reports. The computer exercises should be made in groups of maximum two persons.

 

Software you need to install if you work from your own computer

Note that you can connect to the computers at Chalmers from remote. Please refer to https://it.portal.chalmers.se/itportal/Faq/RemoteAccess?setlang=en for full details. All software should be avilable for the computers in SalA as well as the computer rooms in the Chemistry and Math building.

 

Guidelines for writing and submitting reports

The reports submitted as a group (of maximum two persons) through the Canvas course page. The report should be either in PDF or WORD-format. All of the code necessary should be included in the end of the report as an Appendix. Please double check that the sumibbted code works as intended. Don't forget to add the names and Swedish social security number for all persons in the group at the front page. You only need to submit one report per group.

The reports should contain answers to all the questions posed in the exercise sheet. The answers should almost always have some motivation, meaning that even though the question could be answered with a yes or a no, we require a motivation why. Example question: "Do you see any differences?" Describe the observed differences (if the answer is yes), and not only a yes or a no. When you have been asked to generate a figure, this figure should be included in the report. The reports do not need an introduction, method, results, or discussion section, but should include some information about what has been done. Example: “When doing the quality assessment using fastqc, we saw that…”.

Good luck!


Exam

  • 14 January 2020

Previous exams


Examination
This  course is examined based on,

  • Written exam: 08:30 on January 14, 2020. This gives you 5 hp and determines your grade in the course.
  • Four compulsory computer exercises. When you have passed all four of them you earn 2.5 hp. 

 

Course summary:

Date Details Due